F IDAN with concentration of 105 mM, as compared to the wildtype

F IDAN with concentration of 105 mM, as compared to the wildtype AcN.Screen and Application of Recombinant NitrilasesFigure 1. Process for preparation of IDA from IDAN by chemical reaction. doi:10.1371/journal.pone.0067197.gMaterials and Methods ChemicalsT4 DNA ligase and restriction enzymes were purchased from New England Biolabs (Ipswich, MA). DNA polymerase was obtained from Promega (Madison, WI). pET-28b(+) expression vector was purchased from Novagen (Darmstadt, Germany). Iminodiacetonitrile (IDAN) and iminodiacetic acid (IDA) was obtained from Sigma (St. Louis, MO). All other reagents and chemicals were commercially available and of analytic grade.Acidovorax facilis (AcN) (GeneBank accession no. DQ444267), Alcaligene fecalis And 2B; Supplemental Figure 1).TNFa levels remained higher in IRAK-M2/2 cells ZJUTB10 (AkN) (GeneBank accession no. HQ407378), Arthrobacter pascens (ApN) (GeneBank accession no. AB573018), Burkholderia graminis C4D1M (BgN) (GeneBank accession no. NZ_ABLD01000011), Geobacillus pallidus (GpN) (GeneBank accession no. DQ826045), Rhodococcus rhodochrous J1 (RjN) (GeneBank accession no. D11425), Rhodococcus rhodochrous K22 (RkN) (GeneBank accession no. D12583), and Thalassiosira pseudonana (TpN) (GeneBank accession no. XM_002290007) were synthesized according to the reported methods [18,19]. DNA manipulation, plasmid isolation, and agarose gel electrophoresis were operated according to standard protocol unless additionally stated.Cloning of Nitrilase Genes and Site Directed MutagenesisPrimers for PCR amplification are listed in Table S1. Reactions were performed on a Thermocycler (Bio-Rad, Hercules, CA) using 20 ng genomic DNA. One PCR cycle consisted of the following: 94uC for 45 s, 55?5uC for 90 s, and 72uC for 3 min. The total cycle number was 35 with a final elongation step at 72uC for 10 min. PCR products were then separated on a 1 agarose gel, purified and then cloned into the pET-28b(+) expression vector. Mutagenesis experiments were performed directly on pET-28b(+)?AcN vector according to the published method [20]. The primer pairs designed for mutations are shown in Table S2. One mutagenic PCR cycle consisted of the following: 98uC for 10 s, 55uC for 15 s, and 72uC for 6 min, prior to the mutagenic cycles the reaction was incubated at 94uC for 10 min. Following the PCR, the reactions were treated with 1 U DpnI and incubated for 4 h at 37uC [21]. DNA was purified using QIAquick PCR Purification Kit (Qiagen, Valencia, CA). All pET-28b(+) it constructs were Title Loaded From File transformed into E. coli BL21 (DE3) by heat shock method [22].Nitrilase IdentificationAll gene and protein sequences used in this study were obtained from the Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI). The nitrilase genes fromEnzymes ExpressionFor enzyme expression, E. coli BL21(DE3) cells were selected as the host organism. A single transformed BL21 colony bearing pET-28b(+) it plasmid was used to inoculate 5 mL of in Lysogeny-Broth (LB) containing 50 mg/mL kanamycin (Kan) and then cultured overnight at 37uC. 1 mL of culture was transferred to 1 L of LB containing 50 mg/mL Kan. The culture was grown at 37uC, 325 rpm until the optical density at 600nm was between 0.6 and 0.8. The culture medium was then supplemented with 0.1 mM isopropyl-b-D-thiogalactopyranoside (IPTG), to induce protein expression. Cells were then incubated at 28uC forFigure 2. Multiple sequence alignment of nitrilase sequences. Highlighted in green are catalytic residues, previously described mutations in yellow (41, 42), an.F IDAN with concentration of 105 mM, as compared to the wildtype AcN.Screen and Application of Recombinant NitrilasesFigure 1. Process for preparation of IDA from IDAN by chemical reaction. doi:10.1371/journal.pone.0067197.gMaterials and Methods ChemicalsT4 DNA ligase and restriction enzymes were purchased from New England Biolabs (Ipswich, MA). DNA polymerase was obtained from Promega (Madison, WI). pET-28b(+) expression vector was purchased from Novagen (Darmstadt, Germany). Iminodiacetonitrile (IDAN) and iminodiacetic acid (IDA) was obtained from Sigma (St. Louis, MO). All other reagents and chemicals were commercially available and of analytic grade.Acidovorax facilis (AcN) (GeneBank accession no. DQ444267), Alcaligene fecalis ZJUTB10 (AkN) (GeneBank accession no. HQ407378), Arthrobacter pascens (ApN) (GeneBank accession no. AB573018), Burkholderia graminis C4D1M (BgN) (GeneBank accession no. NZ_ABLD01000011), Geobacillus pallidus (GpN) (GeneBank accession no. DQ826045), Rhodococcus rhodochrous J1 (RjN) (GeneBank accession no. D11425), Rhodococcus rhodochrous K22 (RkN) (GeneBank accession no. D12583), and Thalassiosira pseudonana (TpN) (GeneBank accession no. XM_002290007) were synthesized according to the reported methods [18,19]. DNA manipulation, plasmid isolation, and agarose gel electrophoresis were operated according to standard protocol unless additionally stated.Cloning of Nitrilase Genes and Site Directed MutagenesisPrimers for PCR amplification are listed in Table S1. Reactions were performed on a Thermocycler (Bio-Rad, Hercules, CA) using 20 ng genomic DNA. One PCR cycle consisted of the following: 94uC for 45 s, 55?5uC for 90 s, and 72uC for 3 min. The total cycle number was 35 with a final elongation step at 72uC for 10 min. PCR products were then separated on a 1 agarose gel, purified and then cloned into the pET-28b(+) expression vector. Mutagenesis experiments were performed directly on pET-28b(+)?AcN vector according to the published method [20]. The primer pairs designed for mutations are shown in Table S2. One mutagenic PCR cycle consisted of the following: 98uC for 10 s, 55uC for 15 s, and 72uC for 6 min, prior to the mutagenic cycles the reaction was incubated at 94uC for 10 min. Following the PCR, the reactions were treated with 1 U DpnI and incubated for 4 h at 37uC [21]. DNA was purified using QIAquick PCR Purification Kit (Qiagen, Valencia, CA). All pET-28b(+) it constructs were transformed into E. coli BL21 (DE3) by heat shock method [22].Nitrilase IdentificationAll gene and protein sequences used in this study were obtained from the Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI). The nitrilase genes fromEnzymes ExpressionFor enzyme expression, E. coli BL21(DE3) cells were selected as the host organism. A single transformed BL21 colony bearing pET-28b(+) it plasmid was used to inoculate 5 mL of in Lysogeny-Broth (LB) containing 50 mg/mL kanamycin (Kan) and then cultured overnight at 37uC. 1 mL of culture was transferred to 1 L of LB containing 50 mg/mL Kan. The culture was grown at 37uC, 325 rpm until the optical density at 600nm was between 0.6 and 0.8. The culture medium was then supplemented with 0.1 mM isopropyl-b-D-thiogalactopyranoside (IPTG), to induce protein expression. Cells were then incubated at 28uC forFigure 2. Multiple sequence alignment of nitrilase sequences. Highlighted in green are catalytic residues, previously described mutations in yellow (41, 42), an.